Java Code Examples for java.util.HashMap#get()

/**
 * Gets document parameters and return a string in the form &param1=value1&param2=value2 ...
 * 
 * @param drillParameters the drill parameters
 * 
 * @return the document_ parameters
 */

public String getDocument_Parameters(HashMap<String, DrillParameter> _drillParametersMap) { 
	logger.debug("IN");
	String document_parameter="";
	if(_drillParametersMap!=null){
		for (Iterator iterator = _drillParametersMap.keySet().iterator(); iterator.hasNext();) {
			String name = (String) iterator.next();
			DrillParameter drillPar=(DrillParameter)_drillParametersMap.get(name);
			String value=drillPar.getValue();
			if(name!=null && !name.equals("") && value!=null && !value.equals("")){
				document_parameter+="%26"+name+"%3D"+value;
				//document_parameter+="&"+name+"="+value;
			}
		}
	} 
	logger.debug("OUT");
	return document_parameter;
}
 

private void testCategoricalOutput()
{
	HashMap<MatrixValue.CellIndex, Double> dmlfileC = readDMLMatrixFromHDFS("C");
	HashMap<MatrixValue.CellIndex, Double> rfileC  = readRMatrixFromFS("C");

	// compare categorical imputations
	int countTrue = 0;
	for (MatrixValue.CellIndex index : dmlfileC.keySet()) {
		Double v1 = dmlfileC.get(index);
		Double v2 = rfileC.get(index);
		if(v1.equals(v2))
			countTrue++;
	}

	if(countTrue / (double)dmlfileC.size() > 0.98)
		Assert.assertTrue(true);
	else
		Assert.fail();
}
 

/**
 * Creates a UsernameIterator object.
 *
 * @param patterns The patterns to be evaluated as a String array.
 * @param userData The user information, the required fields are at least first name and last
 *        name.
 * @throws Exception
 */
public UsernameIterator(String[] patterns, HashMap<String, String> userData) throws Exception {
  if (userData == null || patterns == null) {
    throw new Exception("The patterns and userData parameters can't be set as null.");
  }
  if (!userData.containsKey(UsernameManager.FIRST_NAME)
      || !userData.containsKey(UsernameManager.LAST_NAME)) {
    throw new Exception(
        "The userData parameter must cointain at least firstname and lastname fields.");
  }
  String firstname = userData.get(UsernameManager.FIRST_NAME);
  String lastname = userData.get(UsernameManager.LAST_NAME);
  if (firstname.length() > UsernameManager.MAX_NAME_LENGTH
      || lastname.length() > UsernameManager.MAX_NAME_LENGTH) {
    throw new Exception("One of the fields exceds the maximum length. 60 (firstname,lastname).");
  }
  this.patterns = patterns;
  this.userData = userData;
  autonumeric = 1;
  patternIndex = 0;
}
 

private void findLeafPage(BTreePage p, HashMap<PageOperationHandler, Integer> map, AtomicLong leafPageCount) {
    if (p.isNode()) {
        for (PageReference ref : p.getChildren()) {
            BTreePage child = ref.getPage();
            if (child.isLeaf()) {
                PageOperationHandler handler = child.getHandler();
                // System.out.println("handler: " + handler);
                Integer count = map.get(handler);
                if (count == null)
                    count = 1;
                else
                    count++;
                map.put(handler, count);
                leafPageCount.incrementAndGet();
            } else {
                findLeafPage(child, map, leafPageCount);
            }
        }
    }
}
 

/**
 * The following task is used for client Q conflation tests. Similar to
 * checkForConflation task but the task fails if the individual client events
 * are not conflated. (checkForConflation validation pass if there is atleast
 * one event conflated in the total test.
 */
public static void checkClientConflation() {

  PoolImpl pool = HAClientQueue.mypool;
  ClientProxyMembershipID cpm = pool.getProxyID();
  String proxyIdStr = cpm.toString();
  Log.getLogWriter().info("Proxy String : " + proxyIdStr);

  HashMap mp = (HashMap)HAClientQueueBB.getBB().getSharedMap()
      .get(proxyIdStr);

  Long numOfPuts = (Long)mp.get("eventsPut");
  Long numOfConflated = (Long)mp.get("eventsConflated");
  Long numOfMissRemovals = (Long)mp.get("numVoidRemovals");

  Log.getLogWriter().info("value of numOfConflated : " + numOfConflated);

  long totalConflation = HAClientQueueBB.getBB().getSharedCounters().read(
      HAClientQueueBB.NUM_GLOBAL_CONFLATE);
  Log.getLogWriter().info("Total Conflation : " + totalConflation);
  if (numOfConflated.equals(new Long(0))) {
    throw new TestException("No conflation done - Test Issue - needs tuning ");
  }
}
 

/**
 * Checks that there are no duplicates and that all prior prefs have a value
 * @param lst List of values
 * @return true if checks ok, false otherwise
 */
public boolean checkPrefs(List... lst) {
    
    HashMap map = new HashMap();
    for(int i=0; i<lst[0].size(); i++) {
        String value = ((String) lst[0].get(i));
        // No selection made - ignore
        if( value==null || value.trim().equals(Preference.BLANK_PREF_VALUE)) {
            continue;
        }
        // Add additional columns, when present
        for (int j = 1; j < lst.length; j++)
        	value += "|" + ((String)lst[j].get(i));
        
        // Duplicate selection made
        if(map.get(value.trim())!=null) {
            // lst[0].set(i, Preference.BLANK_PREF_VALUE);
            return false;
        }
        map.put(value, value);
    }
    return true;
}
 

private static HashMap<Integer, List<Report>> filterReports() {
    HashMap<Integer, List<Report>> filteredReportsByApp = new HashMap<>();
    HashSet<String> filterMap = new HashSet<>();
    String address;
    ArrayList<Report> list;
    ArrayList<Report> filteredList;
    for (int key : mUidReportMap.keySet()) {
        filteredReportsByApp.put(key, new ArrayList<Report>());
        list = (ArrayList<Report>) mUidReportMap.get(key);
        filteredList = (ArrayList<Report>) filteredReportsByApp.get(key);
        filterMap.clear();
        for (int i = 0; i < list.size(); i++) {
            address = list.get(i).remoteAdd.getHostAddress();
            if (!filterMap.contains(address)) {
                filteredList.add(list.get(i));
                filterMap.add(address);
            }
        }
    }
    return filteredReportsByApp;
}
 

@RunAsClient
@Test(groups = TEST_GROUP_CDI_JSON,
    description = "Verify that the injected iat claim is as expected from Token2")
public void verifyInjectedIssuedAt2() throws Exception {
    Reporter.log("Begin verifyInjectedIssuedAt2\n");
    HashMap<String, Long> timeClaims = new HashMap<>();
    String token2 = TokenUtils.generateTokenString("/Token2.json", null, timeClaims);
    Long iatClaim = timeClaims.get(Claims.auth_time.name());
    Long authTimeClaim = timeClaims.get(Claims.auth_time.name());
    String uri = baseURL.toExternalForm() + "endp/verifyInjectedIssuedAt";
    WebTarget echoEndpointTarget = ClientBuilder.newClient()
        .target(uri)
        .queryParam(Claims.iat.name(), iatClaim)
        .queryParam(Claims.auth_time.name(), authTimeClaim);
    Response response = echoEndpointTarget.request(MediaType.APPLICATION_JSON).header(HttpHeaders.AUTHORIZATION, "Bearer " + token2).get();
    Assert.assertEquals(response.getStatus(), HttpURLConnection.HTTP_OK);
    String replyString = response.readEntity(String.class);
    JsonReader jsonReader = Json.createReader(new StringReader(replyString));
    JsonObject reply = jsonReader.readObject();
    Reporter.log(reply.toString());
    Assert.assertTrue(reply.getBoolean("pass"), reply.getString("msg"));
}
 

/** Reconstruct from an XML entry. */
public LayerSet(final Project project, final long id, final HashMap<String,String> ht_attributes, final HashMap<Displayable,String> ht_links) {
	super(project, id, ht_attributes, ht_links);
	String data;
	if (null != (data = ht_attributes.get("layer_width"))) this.layer_width = Float.parseFloat(data);
	else xmlError("layer_width", this.layer_width);
	if (null != (data = ht_attributes.get("layer_height"))) this.layer_height = Float.parseFloat(data);
	else xmlError("layer_height", this.layer_height);
	if (null != (data = ht_attributes.get("rot_x"))) this.rot_x = Double.parseDouble(data);
	else xmlError("rot_x", this.rot_x);
	if (null != (data = ht_attributes.get("rot_y"))) this.rot_y = Double.parseDouble(data);
	else xmlError("rot_y", this.rot_y);
	if (null != (data = ht_attributes.get("rot_z"))) this.rot_y = Double.parseDouble(data);
	else xmlError("rot_z", this.rot_z);
	if (null != (data = ht_attributes.get("snapshots_quality"))) snapshots_quality = Boolean.valueOf(data.trim().toLowerCase());
	if (null != (data = ht_attributes.get("snapshots_mode"))) {
		final String smode = data.trim();
		for (int i=0; i<snapshot_modes.length; i++) {
			if (smode.equals(snapshot_modes[i])) {
				snapshots_mode = i;
				break;
			}
		}
	}
	if (null != (data = ht_attributes.get("color_cues"))) color_cues = Boolean.valueOf(data.trim().toLowerCase());
	if (null != (data = ht_attributes.get("area_color_cues"))) area_color_cues = Boolean.valueOf(data.trim().toLowerCase());
	if (null != (data = ht_attributes.get("n_layers_color_cue"))) {
		n_layers_color_cue = Integer.parseInt(data.trim().toLowerCase());
		if (n_layers_color_cue < -1) n_layers_color_cue = -1;
	}
	if (null != (data = ht_attributes.get("avoid_color_cue_colors"))) {
		// If there's any error in the parsing, default to true for use_color_cue_colors:
		use_color_cue_colors = !Boolean.valueOf(data.trim().toLowerCase());
	}
	if (null != (data = ht_attributes.get("paint_arrows"))) paint_arrows = Boolean.valueOf(data.trim().toLowerCase());
	if (null != (data = ht_attributes.get("paint_tags"))) paint_tags = Boolean.valueOf(data.trim().toLowerCase());
	if (null != (data = ht_attributes.get("paint_edge_confidence_boxes"))) paint_edge_confidence_boxes = Boolean.valueOf(data.trim().toLowerCase());
	if (null != (data = ht_attributes.get("prepaint"))) prepaint = Boolean.valueOf(data.trim().toLowerCase());
	if (null != (data = ht_attributes.get("preload_ahead"))) preload_ahead = Integer.parseInt(data);
}
 

public void applyGraphResults(DirectedGraph graph, HashMap map){
	Node node = (Node)map.get(this);
	((CFGNodeFigure)getFigure()).setBounds(new Rectangle(node.x, node.y, node.width, node.height));//getFigure().getBounds().height));//getFigure().getBounds().height));
	List outgoing = getSourceConnections();
	for (int i = 0; i < outgoing.size(); i++){
		CFGEdgeEditPart edge = (CFGEdgeEditPart)outgoing.get(i);
		edge.applyGraphResults(graph, map);
	}

}
 

private static boolean isAValidCategoryOptionCombo(
        HashMap<String, List<CategoryCombo>> dataElementCategoryOptionRelation, Field field) {
    for (CategoryCombo categoryCombo : dataElementCategoryOptionRelation.get(
            field.getDataElement())) {
        for (String categoryOptionComboUId : categoryCombo.getCategoryOptionComboUIdList()) {
            if (field.getCategoryOptionCombo().equals(categoryOptionComboUId)) {
                return true;
            }
        }
    }
    return false;
}
 

/**
 * Returns the setter or getter requested. This utility function checks whether the
 * requested method exists in the propertyMapMap cache. If not, it calls another
 * utility function to request the Method from the targetClass directly.
 * @param targetClass The Class on which the requested method should exist.
 * @param propertyMapMap The cache of setters/getters derived so far.
 * @param prefix "set" or "get", for the setter or getter.
 * @param valueType The type of parameter passed into the method (null for getter).
 * @return Method the method associated with mPropertyName.
 */
private Method setupSetterOrGetter(Class targetClass,
        HashMap<Class, HashMap<String, Method>> propertyMapMap,
        String prefix, Class valueType) {
    Method setterOrGetter = null;
    try {
        // Have to lock property map prior to reading it, to guard against
        // another thread putting something in there after we've checked it
        // but before we've added an entry to it
        mPropertyMapLock.writeLock().lock();
        HashMap<String, Method> propertyMap = propertyMapMap.get(targetClass);
        if (propertyMap != null) {
            setterOrGetter = propertyMap.get(mPropertyName);
        }
        if (setterOrGetter == null) {
            setterOrGetter = getPropertyFunction(targetClass, prefix, valueType);
            if (propertyMap == null) {
                propertyMap = new HashMap<String, Method>();
                propertyMapMap.put(targetClass, propertyMap);
            }
            propertyMap.put(mPropertyName, setterOrGetter);
        }
    } finally {
        mPropertyMapLock.writeLock().unlock();
    }
    return setterOrGetter;
}
 

@SuppressWarnings("unchecked")
private static boolean checkTokenizer(Class<? extends TokenizerFactory> tokenizerFactoryClass, Map<String, Object> fieldTypeInfoMap) {
  HashMap<String, Object> analyzer = (HashMap<String, Object>) fieldTypeInfoMap.get("analyzer");
  HashMap<String, Object> tokenizerMap = (HashMap<String, Object>)MapUtils.getObject(analyzer, "tokenizer");
  if (tokenizerMap != null) {
    String tokenizerClass = (String) tokenizerMap.get("class");
    if (StringUtils.isNotEmpty(tokenizerClass)) {
      tokenizerClass = tokenizerClass.replace("solr.", "");
      return tokenizerClass.equalsIgnoreCase(tokenizerFactoryClass.getSimpleName());
    }
  }
  
  return false;
}
 

@Override
public void setGeopaparazziProjectViewerPreferencesMap( HashMap<String, String> prefsMap ) {
    Preferences preferences = Preferences.userRoot().node(PreferencesHandler.PREFS_NODE_NAME);
    String lastPath = prefsMap.get(LAST_GP_PROJECTS_PATH);
    preferences.put(LAST_GP_PROJECTS_PATH, lastPath);
}
 

/**
 * Expand labels by a given factor
 * @param image  input label image
 * @param ratio  percentage of expansion (values between 0 and 100)
 * @return expanded image
 */
public static final ImageStack expandLabels(ImageStack image,
		float ratio) 
{
	// size of input image
	int sizeX = image.getWidth();
	int sizeY = image.getHeight();
	int sizeZ = image.getSize();
	
	// size of result image
	int sizeX2 = (int) Math.round(sizeX * (1. + ratio / 100));
	int sizeY2 = (int) Math.round(sizeY * (1. + ratio / 100));
	int sizeZ2 = (int) Math.round(sizeZ * (1. + ratio / 100));
	
	// allocate memory for result
	int bitDepth = image.getBitDepth();
	ImageStack result = ImageStack.create(sizeX2, sizeY2, sizeZ2, bitDepth);

	// compute centroids of labels
	int[] labels = LabelImages.findAllLabels(image);
	double[][] centroids = Centroid3D.centroids(image, labels);
	
	// compute shift associated to each label
	int nLabels = labels.length;
	int[][] shifts = new int[nLabels][3];
	for (int i = 0; i < nLabels; i++)
	{
		shifts[i][0] = (int) Math.floor(centroids[i][0] * ratio / 100);
		shifts[i][1] = (int) Math.floor(centroids[i][1] * ratio / 100);
		shifts[i][2] = (int) Math.floor(centroids[i][2] * ratio / 100);
	}
	
       // create associative array to know index of each label
	HashMap<Integer, Integer> labelIndices = new HashMap<Integer, Integer>();
       for (int i = 0; i < nLabels; i++) 
       {
       	labelIndices.put(labels[i], i);
       }

       for (int z = 0; z < sizeZ; z++)
       {
       	for (int y = 0; y < sizeY; y++)
       	{
       		for (int x = 0; x < sizeX; x++)
       		{
       			double label = image.getVoxel( x, y, z );
       			if ( Double.compare( label,  0 ) == 0 )
       				continue;

       			int index = labelIndices.get( (int) label );
       			int x2 = x + shifts[index][0];
       			int y2 = y + shifts[index][1];
       			int z2 = z + shifts[index][2];
       			result.setVoxel( x2, y2, z2, label );
       		}
       	}
       }

	return result;
}
 

public static ArrayList<ModelFamilyEC> getActiveModels() {
	ArrayList<ModelFamilyEC> modelFamilies = new ArrayList<>();
	Connection conn = null;
	PreparedStatement sql = null;
	ResultSet result = null;

	try {
		conn = getMySqlConnection();

		Statement sql2 = conn.createStatement();
		sql2.execute("SET group_concat_max_len = 10240");
		sql2.close();

		sql = conn
				.prepareStatement(
						"SELECT \n"
								+ " fam.modelFamilyID, \n"
								+ "	fam.crisisID, \n"
								+ "	col.code AS crisisCode, \n"
								+ "	col.name AS crisisName, \n"
								+ "	fam.nominalAttributeID, \n"
								+ "	attr.code AS nominalAttributeCode, \n"
								+ "	attr.name AS nominalAttributeName, \n"
								+ "	attr.description AS nominalAttributeDescription, \n"
								+ " mdl.modelID, \n"
								+ "	lbl.nominalLabelID,\n"
								+ "	lbl.nominalLabelCode,\n"
								+ "	lbl.name as nominalLabelName,\n"
								+ "	lbl.description as nominLabelDescription, \n"
								+ "	COUNT(DISTINCT dnl.documentID) AS labeledItemCount\n"
								+ "FROM model_family fam \n"
								+ "LEFT JOIN model mdl on mdl.modelFamilyID = fam.modelFamilyID \n"
								+ "JOIN collection col on col.id = fam.crisisID and col.classifier_enabled = 1 \n"
								+ "JOIN nominal_attribute attr ON attr.nominalAttributeID = fam.nominalAttributeID \n"
								+ "JOIN nominal_label lbl ON lbl.nominalAttributeID = fam.nominalAttributeID \n"
								+ "LEFT JOIN document doc ON doc.crisisID=fam.crisisID \n"
								+ "LEFT JOIN document_nominal_label dnl ON dnl.documentID=doc.documentID AND dnl.nominalLabelID=lbl.nominalLabelID \n"
								+ "WHERE fam.isActive AND (mdl.modelID IS NULL OR mdl.isCurrentModel) \n"
								+ "GROUP BY crisisID, nominalAttributeID, nominalLabelID ");
		result = sql.executeQuery();

		ModelFamilyEC family = null;
		NominalAttributeEC attribute = null;
		HashMap<ModelFamilyEC, Integer> familyLabelCount = new HashMap<>();
		while (result.next()) {
			if (family == null || family.getModelFamilyID() != result.getInt("modelFamilyID")) {

				//create attribute
				attribute = new NominalAttributeEC();
				attribute.setNominalAttributeID(result.getInt("nominalAttributeID"));
				attribute.setCode(result.getString("nominalAttributeCode"));
				attribute.setDescription(result.getString("nominalAttributeDescription"));
				attribute.setName(result.getString("nominalAttributeName"));

				//create model family
				family = new ModelFamilyEC();
				family.setCrisisID(result.getInt("crisisID"));
				int tmpModelID = result.getInt("modelID");
				if (!result.wasNull()) {
					family.setCurrentModelID(tmpModelID);
				}
				family.setIsActive(true);
				family.setModelFamilyID(result.getInt("modelFamilyID"));
				family.setNominalAttribute(attribute);

				familyLabelCount.put(family, 0);
				modelFamilies.add(family);
			}

			//create label
			NominalLabelEC label = new NominalLabelEC();
			label.setDescription(result.getString("nominLabelDescription"));
			label.setName(result.getString("nominalLabelName"));
			label.setNominalAttribute(attribute);
			label.setNominalLabelCode(result.getString("nominalLabelCode"));
			label.setNominalLabelID(result.getInt("nominalLabelID"));
			attribute.addNominalLabel(label);

			int count = familyLabelCount.get(family);
			familyLabelCount.put(family, count + result.getInt("labeledItemCount"));

		}

		//sum training sample counts per attribute
		for (Map.Entry<ModelFamilyEC, Integer> entry : familyLabelCount.entrySet()) {
			entry.getKey().setTrainingExampleCount(entry.getValue());
		}

	} catch (SQLException e) {
		logger.error("Exception when getting model state", e);
	} finally {
		close(result);
		close(sql);
		close(conn);
	}

	return modelFamilies;
}
 

@Execute
public void process() throws Exception {
    checkNull(inElev);
    // extract some attributes of the map
    HashMap<String, Double> attribute = CoverageUtilities.getRegionParamsFromGridCoverage(inElev);
    double dx = attribute.get(CoverageUtilities.XRES);
    CoverageUtilities.getRegionParamsFromGridCoverage(inElev);
    // extract the raster.
    RenderedImage pitTmpRI = inElev.getRenderedImage();
    WritableRaster pitWR = CoverageUtilities.replaceNovalue(pitTmpRI, -9999.0);
    pitTmpRI = null;
    minX = pitWR.getMinX();
    minY = pitWR.getMinY();
    rows = pitWR.getHeight();
    cols = pitWR.getWidth();

    WritableRaster skyWR = skyviewfactor(pitWR, dx);

    int maxY = minY + rows;
    int maxX = minX + cols;
    for( int y = minY + 2; y < maxY - 2; y++ ) {
        for( int x = minX + 2; x < maxX - 2; x++ ) {
            if (pitWR.getSampleDouble(x, y, 0) == -9999.0) {
                skyWR.setSample(x, y, 0, doubleNovalue);
            }
        }
    }
    for( int y = minY; y < maxY; y++ ) {
        skyWR.setSample(0, y, 0, doubleNovalue);
        skyWR.setSample(1, y, 0, doubleNovalue);
        skyWR.setSample(cols - 2, y, 0, doubleNovalue);
        skyWR.setSample(cols - 1, y, 0, doubleNovalue);
    }

    for( int x = minX + 2; x < maxX - 2; x++ ) {
        skyWR.setSample(x, 0, 0, doubleNovalue);
        skyWR.setSample(x, 1, 0, doubleNovalue);
        skyWR.setSample(x, rows - 2, 0, doubleNovalue);
        skyWR.setSample(x, rows - 1, 0, doubleNovalue);
    }
    outSky = CoverageUtilities.buildCoverage("skyview factor", skyWR, attribute, inElev.getCoordinateReferenceSystem());

}
 

/**
 * Computes the bounding box of each region within a 3D label image.
 * 
 * @param image
 *            the input image containing label of particles
 * @param labels
 *            the array of labels within the image
 * @param calib
 *            the calibration of the image
 * @return an array of Box3D representing the calibrated coordinates of
 *         the bounding box of each region
 */
public Box3D[] analyzeRegions(ImageStack image, int[] labels, Calibration calib)
{
	// size of image
	int sizeX = image.getWidth();
	int sizeY = image.getHeight();
	int sizeZ = image.getSize();

	// Extract spatial calibration
	double sx = 1, sy = 1, sz = 1;
	double ox = 0, oy = 0, oz = 0;
	if (calib != null)
	{
		sx = calib.pixelWidth;
		sy = calib.pixelHeight;
		sz = calib.pixelDepth;
		ox = calib.xOrigin;
		oy = calib.yOrigin;
		oz = calib.zOrigin;
	}
	
	// create associative array to know index of each label
       HashMap<Integer, Integer> labelIndices = LabelImages.mapLabelIndices(labels);

	// allocate memory for result
	int nLabels = labels.length;
	double[] xmin = new double[nLabels];
	double[] xmax = new double[nLabels];
	double[] ymin = new double[nLabels];
	double[] ymax = new double[nLabels];
	double[] zmin = new double[nLabels];
	double[] zmax = new double[nLabels];
	
	// initialize to extreme values
	for (int i = 0; i < nLabels; i++)
	{
		xmin[i] = Double.POSITIVE_INFINITY;
		xmax[i] = Double.NEGATIVE_INFINITY;
		ymin[i] = Double.POSITIVE_INFINITY;
		ymax[i] = Double.NEGATIVE_INFINITY;
		zmin[i] = Double.POSITIVE_INFINITY;
		zmax[i] = Double.NEGATIVE_INFINITY;
	}

	// compute extreme coordinates of each region
   	fireStatusChanged(this, "Compute bounds");
   	for (int z = 0; z < sizeZ; z++) 
   	{
   		for (int y = 0; y < sizeY; y++) 
   		{
   			for (int x = 0; x < sizeX; x++)
   			{
   				int label = (int) image.getVoxel(x, y, z);
   				if (label == 0)
   					continue;

                   // do not process labels that are not in the input list 
                   if (!labelIndices.containsKey(label))
                       continue;
   				int index = labelIndices.get(label);

   				xmin[index] = Math.min(xmin[index], x);
   				xmax[index] = Math.max(xmax[index], x + 1);
   				ymin[index] = Math.min(ymin[index], y);
   				ymax[index] = Math.max(ymax[index], y + 1);
   				zmin[index] = Math.min(zmin[index], z);
   				zmax[index] = Math.max(zmax[index], z + 1);
   			}
   		}
   	}
   	
	// create bounding box instances
	Box3D[] boxes = new Box3D[nLabels];
	for (int i = 0; i < nLabels; i++)
	{
		boxes[i] = new Box3D(
				xmin[i] * sx + ox, xmax[i] * sx + ox,
				ymin[i] * sy + oy, ymax[i] * sy + oy, 
				zmin[i] * sz + oz, zmax[i] * sz + oz);
	}
	return boxes;
}
 

public void startElement(String namespace_URI, String local_name, String qualified_name, Attributes attributes) throws SAXException {
	if (null == loader) return;

	//Utils.log2("startElement: " + qualified_name);
	this.counter++;
	if (0 == counter % 100) { // davi-experimenting: don't talk so much when you have > 600,000 patches to load!
		Utils.showStatus("Loading " + counter, false);
	}
	try {
		// failsafe:
		qualified_name = qualified_name.toLowerCase();

		final HashMap<String,String> ht_attributes = new HashMap<String,String>();
		for (int i=attributes.getLength() -1; i>-1; i--) {
			ht_attributes.put(attributes.getQName(i).toLowerCase(), attributes.getValue(i));
		}
		// get the id, which whenever possible it's the id of the encapsulating Thing object. The encapsulated object id is the oid
		// The type is specified by the qualified_name
		Thing thing = null;
		if (0 == qualified_name.indexOf("t2_")) {
			if (qualified_name.equals("t2_display")) {
				if (open_displays) al_displays.add(ht_attributes); // store for later, until the layers exist
			} else {
				// a Layer, LayerSet or Displayable object
				thing = makeLayerThing(qualified_name, ht_attributes);
				if (null != thing) {
					if (null == root_lt && thing.getObject() instanceof LayerSet) {
						root_lt = (LayerThing)thing;
					}
				}
			}
		} else if (qualified_name.equals("project")) {
			if (null != this.root_pt) {
				Utils.log("WARNING: more than one project definitions.");
				return;
			}
			// Create the project
			this.project = new Project(Long.parseLong(ht_attributes.remove("id")), ht_attributes.remove("title"));
			this.project.setTempLoader(this.loader); // temp, but will be the same anyway
			this.project.parseXMLOptions(ht_attributes);
			this.project.addToDatabase(); // register id
			String title = ht_attributes.get("title");
			if (null != title) this.project.setTitle(title);
			// Add all unique TemplateThing types to the project
			for (Iterator<TemplateThing> it = root_tt.getUniqueTypes(new HashMap<String,TemplateThing>()).values().iterator(); it.hasNext(); ) {
				this.project.addUniqueType(it.next());
			}
			this.project.addUniqueType(this.project_tt);
			this.root_pt = new ProjectThing(this.project_tt, this.project, this.project);
			// Add a project pointer to all template things
			this.root_tt.addToDatabase(this.project);
			thing = root_pt;
		} else if (qualified_name.startsWith("ict_transform")||qualified_name.startsWith("iict_transform")) {
			makeCoordinateTransform(qualified_name, ht_attributes);
		} else if (!qualified_name.equals("trakem2")) {
			// Any abstract object
			thing = makeProjectThing(qualified_name, ht_attributes);
		}
		if (null != thing) {
			// get the previously open thing and add this new_thing to it as a child
			int size = al_open.size();
			if (size > 0) {
				Thing parent = al_open.get(size -1);
				parent.addChild(thing);
				//Utils.log2("Adding child " + thing + " to parent " + parent);
			}
			// add the new thing as open
			al_open.add(thing);
		}
	} catch (Exception e) {
		IJError.print(e);
		skip = true;
	}
}
 

/**
 * Registers standard transliterators with the system.  Called by
 * Transliterator during initialization.  Scan all current targets
 * and register those that are scripts T as Any-T/V.
 */
static void register() {

    HashMap<String, Set<String>> seen = new HashMap<String, Set<String>>(); // old code used set, but was dependent on order

    for (Enumeration<String> s = Transliterator.getAvailableSources(); s.hasMoreElements(); ) {
        String source = s.nextElement();

        // Ignore the "Any" source
        if (source.equalsIgnoreCase(ANY)) continue;

        for (Enumeration<String> t = Transliterator.getAvailableTargets(source);
             t.hasMoreElements(); ) {
            String target = t.nextElement();

            // Get the script code for the target.  If not a script, ignore.
            int targetScript = scriptNameToCode(target);
            if (targetScript == UScript.INVALID_CODE) {
                continue;
            }

            Set<String> seenVariants = seen.get(target);
            if (seenVariants == null) {
                seen.put(target, seenVariants = new HashSet<String>());
            }

            for (Enumeration<String> v = Transliterator.getAvailableVariants(source, target);
                 v.hasMoreElements(); ) {
                String variant = v.nextElement();

                // Only process each target/variant pair once
                if (seenVariants.contains(variant)) {
                    continue;
                }
                seenVariants.add(variant);

                String id;
                id = TransliteratorIDParser.STVtoID(ANY, target, variant);
                AnyTransliterator trans = new AnyTransliterator(id, target, variant,
                                                                targetScript);
                Transliterator.registerInstance(trans);
                Transliterator.registerSpecialInverse(target, NULL_ID, false);
            }
        }
    }
}